Illumina NovaSeq 6000 paired end sequencing
The Hi-C library was prepared following the Arima Protocol “Arima-HiC_AnimalTissue_v00” (Document number A160126 v00). The chromatin was fragmented in an AFA Fiber Crimp-cap microTUBE using a COVARIS E220 with the following settings: Peak Incident Power 175 W, Acoustic Duty Factor 10 %, 200 Cycles Per Burst, 50 s treatment time. The fragmented chromatin was purified using AMPure XP beads and subjected to library preparation following the “Arima-HiC Kit, Library Preparation using Illumina TruSeq DNA PCR-Free Library Prep” Protocol (Document number A160111 v01) and the Arima-kit reagents were supplemented by reagents of an Illumina TruSeq PCR-Free library preparation kit. The library was amplified for 11 cycles using an Illumina TruSeq DNA CD Index. The final library was analysed for fragment length distribution using an Agilent Fragment Analyser with a high sensitivity NGS Fragment 1-6000bp kit and for concentration using the Qubit high sensitivity dsDNA kit. Subsequently the library was sequenced with a depth of approximately 800 million reads on a NovaSeq 6000 S4 flow cell with a read length of 2x150 bp.